"While it will be sad to say goodbye to Mike the good news is that he is putting in place an exciting plan to set up his own business with his wife Stacey", McKerrow said.
"Mike has been planning this move for quite some time but thankfully agreed to delay his move and act in the role of chief infrastructure officer whilst we recruited for our new CIO."
McKerrow said Mendonça will leave a "big hole" in the infrastructure and delivery team.
Mendonça was a critical member of the team that led the city's response and recovery efforts following the 2016 Kaikōura earthquake, McKerrow said.
"As a result of that event, his team successfully ensured that 113 buildings which had unreinforced masonry parapets and facades strengthened across the city within a very tight 18 month period.
"This work has continued with oversight of the regulatory requirement for strengthening of almost 600 earthquake-prone buildings across the city."
McKerrow said Mendonça has contributed a vast amount of expertise to council over the years.
"He has always provided a calm and steady hand even when under great pressure and never shied from going the extra mile to get the job done."
Mendonça will be leaving in early November.